Skip to content

GitLab

Genesys Backend
Genesys Backend
Commit 9a9f0cbc authored by Matija Obreza's avatar Matija Obreza
Browse files
Options

Use Taxonomy2 instead of old Taxonomy

parent 3b99eddf
Hide whitespace changes
Inline Side-by-side
Showing with 88 additions and 85 deletions
src/main/java/org/genesys2/server/model/genesys/Accession.java
View file @ 9a9f0cbc
......@@ -23,7 +23,6 @@ import javax.persistence.Entity;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
import org.genesys2.server.lucene.genesys.AccessionBridge;
import org.genesys2.server.model.VersionedAuditedModel;
......@@ -33,7 +32,10 @@ import org.hibernate.search.annotations.ClassBridge;
import org.hibernate.search.annotations.Indexed;
@Entity
@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(columnNames = { "instCode", "acceNumb", "genus" }) })
@Table(name = "accession")
// TODO FIXME Reenable
// @Table(name = "accession", uniqueConstraints = {
// @UniqueConstraint(columnNames = { "instCode", "acceNumb", "taxGenus" }) })
@Indexed
@ClassBridge(name = "body", impl = AccessionBridge.class)
public class Accession extends VersionedAuditedModel {
......@@ -54,11 +56,11 @@ public class Accession extends VersionedAuditedModel {
@ManyToOne(cascade = {}, optional = true)
@JoinColumn(name = "taxonomyId")
private Taxonomy taxonomy;
private Taxonomy taxonomy1;
@ManyToOne(cascade = {}, optional = false)
@JoinColumn(name = "taxonomyId2")
private Taxonomy2 taxonomy2;
private Taxonomy2 taxonomy;
@Column(name = "acqSrc", length = 3)
private String acquisitionSource;
......@@ -136,13 +138,13 @@ public class Accession extends VersionedAuditedModel {
}
public Taxonomy getTaxonomy1() {
return this.taxonomy;
return this.taxonomy1;
}
public Taxonomy2 getTaxonomy() {
return this.taxonomy2;
return this.taxonomy;
}
public String getAcquisitionSource() {
return this.acquisitionSource;
}
......@@ -231,7 +233,6 @@ public class Accession extends VersionedAuditedModel {
this.mlsStatus = mlsStatus;
}
public long getTaxGenus() {
return taxGenus;
}
......@@ -249,7 +250,11 @@ public class Accession extends VersionedAuditedModel {
}
public void setTaxonomy(Taxonomy2 taxonomy2) {
this.taxonomy2 = taxonomy2;
this.taxonomy = taxonomy2;
}
public void setTaxonomy1(Taxonomy taxonomy1) {
this.taxonomy1 = taxonomy1;
}
@Override
......
src/main/java/org/genesys2/server/persistence/domain/AccessionRepository.java
View file @ 9a9f0cbc
......@@ -38,8 +38,8 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
@Query(countQuery = "select count(*) from accession a where a.institute = ?1")
Page<Accession> findByInstitute(FaoInstitute institute, Pageable pageable);
@Query(countQuery = "select count(*) from accession a where a.genus = ?1")
Page<Accession> findByGenus(String genus, Pageable pageable);
@Query(countQuery = "select count(*) from accession a where a.taxGenus = ?1")
Page<Accession> findByTaxGenus(long taxonomyId, Pageable pageable);
List<Accession> findByInstitute(FaoInstitute institute);
......@@ -53,8 +53,9 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
Page<Object[]> statisticsTaxonomyInInstitute(FaoInstitute institute, Pageable pageable);
// FIXME Slow query
@Query(value = "select ct.crop, count(a) from Accession a inner join a.taxonomy t join t.cropTaxonomies ct where a.institute = ?1 group by ct.crop order by count(a) desc", countQuery = "select count(distinct ct.crop) from Accession a inner join a.taxonomy t join t.cropTaxonomies ct where a.institute = ?1")
Page<Object[]> statisticsCropInInstitute(FaoInstitute institute, Pageable pageable);
// FIXME TOOD taxonomy1!
// @Query(value = "select ct.crop, count(a) from Accession a inner join a.taxonomy1 t join t.cropTaxonomies ct where a.institute = ?1 group by ct.crop order by count(a) desc", countQuery = "select count(distinct ct.crop) from Accession a inner join a.taxonomy t join t.cropTaxonomies ct where a.institute = ?1")
// Page<Object[]> statisticsCropInInstitute(FaoInstitute institute, Pageable pageable);
@Query("select count(a) from Accession a where a.origin = ?1")
long countByOrigin(String isoCode3);
......@@ -65,17 +66,17 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
@Query("select a from Accession a where a.institute in ( ?1 )")
Page<Accession> findByInstitute(List<FaoInstitute> institutes, Pageable pageable);
@Query("select a from Accession a where a.genus in ( ?1 )")
Page<Accession> findByGenus(List<String> genus, Pageable pageable);
// @Query("select a from Accession a where a.genus in ( ?1 )")
// Page<Accession> findByGenus(List<String> genus, Pageable pageable);
@Query("select a.institute, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.institute order by total desc")
List<Object[]> statisticsInstitute(List<String> genus);
// @Query("select a.institute, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.institute order by total desc")
// List<Object[]> statisticsInstitute(List<String> genus);
@Query("select a.origin, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.origin order by total desc")
List<Object[]> statisticsOrigin(List<String> genus);
// @Query("select a.origin, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.origin order by total desc")
// List<Object[]> statisticsOrigin(List<String> genus);
@Query("select a.taxonomy, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.taxonomy order by total desc")
List<Object[]> statisticsTaxonomy(List<String> genus);
// @Query("select a.taxonomy, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.taxonomy order by total desc")
// List<Object[]> statisticsTaxonomy(List<String> genus);
// List<Accession> findByOrigin(String origin);
......@@ -96,9 +97,10 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
@Query("select a from Accession a where a.taxonomy in ( ?1 )")
Page<Accession> findByTaxonomy(Collection<Taxonomy> taxonomies, Pageable pageable);
Accession findByInstituteCodeAndAccessionName(String instCode, String acceNumb);
Accession findByInstituteCodeAndAccessionName(String instCode, String accessionName);
Accession findByInstituteCodeAndAccessionNameAndGenus(String holdingInstitute, String accessionName, String genus);
@Query("select a from Accession a inner join a.taxonomy t where a.instituteCode=?1 and a.accessionName=?2 and t.genus=?3")
Accession findOne(String holdingInstitute, String accessionName, String genus);
@Query("select count(a.id) from Accession a where a.id in ( ?1 ) and a.availability = true")
long countAvailable(Set<Long> accessionIds);
......
src/main/java/org/genesys2/server/service/GenesysService.java
View file @ 9a9f0cbc
......@@ -101,7 +101,7 @@ public interface GenesysService {
Page<Object[]> statisticsTaxonomyByInstitute(FaoInstitute faoInstitute, Pageable pageable);
Page<Object[]> statisticsCropByInstitute(FaoInstitute faoInstitute, Pageable pageable);
// Page<Object[]> statisticsCropByInstitute(FaoInstitute faoInstitute, Pageable pageable);
Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
......
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @ 9a9f0cbc
......@@ -84,6 +84,7 @@ import org.genesys2.server.service.AclService;
import org.genesys2.server.service.DatasetService;
import org.genesys2.server.service.GenesysService;
import org.genesys2.server.service.HtmlSanitizer;
import org.genesys2.server.service.TaxonomyService;
import org.genesys2.server.service.TraitService;
import org.genesys2.spring.SecurityContextUtil;
import org.springframework.beans.factory.annotation.Autowired;
......@@ -130,6 +131,8 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
private MetadataMethodRepository metadataMethodRepository;
@Autowired
private TraitValueRepository traitValueRepository;
@Autowired
private TaxonomyService taxonomyService;
@Autowired
private CropTaxonomyRepository cropTaxonomyRepository;
......@@ -168,7 +171,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
public long countAll() {
return accessionRepository.count();
}
@Override
public long countByInstitute(FaoInstitute institute) {
return accessionRepository.countByInstitute(institute);
......@@ -206,7 +209,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
public List<Accession> listAccessions(List<? extends AccessionIdentifier3> accns) {
List<Accession> result = new ArrayList<Accession>(accns.size());
for (AccessionIdentifier3 aid3 : accns) {
Accession accn = accessionRepository.findByInstituteCodeAndAccessionNameAndGenus(aid3.getHoldingInstitute(), aid3.getAccessionName(),
Accession accn = accessionRepository.findOne(aid3.getHoldingInstitute(), aid3.getAccessionName(),
aid3.getGenus());
// Including null's
result.add(accn);
......@@ -222,9 +225,8 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@Override
public Accession getAccession(AccessionIdentifier3 aid3) {
return accessionRepository.findByInstituteCodeAndAccessionNameAndGenus(aid3.getHoldingInstitute(), aid3.getAccessionName(), aid3.getGenus());
return accessionRepository.findOne(aid3.getHoldingInstitute(), aid3.getAccessionName(), aid3.getGenus());
}
@Override
public Accession getAccession(String instCode, String acceNumb) {
......@@ -233,7 +235,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@Override
public Accession getAccession(String instCode, String acceNumb, String genus) {
return accessionRepository.findByInstituteCodeAndAccessionNameAndGenus(instCode, acceNumb, genus);
return accessionRepository.findOne(instCode, acceNumb, genus);
}
@Override
......@@ -364,11 +366,6 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
return accessionRepository.statisticsTaxonomyInInstitute(institute, pageable);
}
@Override
public Page<Object[]> statisticsCropByInstitute(FaoInstitute institute, Pageable pageable) {
return accessionRepository.statisticsCropInInstitute(institute, pageable);
}
@Override
public Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable) {
return accessionRepository.findByInstituteAndTaxonomy(institute, taxonomy, pageable);
......@@ -381,7 +378,8 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@Override
public Page<Accession> listAccessionsByGenus(String genus, Pageable pageable) {
return accessionRepository.findByGenus(genus, pageable);
long taxGenusId = taxonomyService.getTaxonomy2Id(genus);
return accessionRepository.findByTaxGenus(taxGenusId, pageable);
}
@Override
......@@ -416,7 +414,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
public List<Parameter> listTraits() {
return parameterRepository.findAll(new Sort(new Order(Direction.ASC, "id")));
}
@Override
public Page<Parameter> listTraits(Pageable pageable) {
return parameterRepository.findAll(pageable);
......@@ -446,7 +444,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
public List<Method> listMethods() {
return methodRepository.findAll(new Sort(new Order(Direction.ASC, "id")));
}
@Override
public Page<Method> listMethods(Pageable pageable) {
return methodRepository.findAll(pageable);
......@@ -532,7 +530,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
svalbardRepository.deleteForAccessions(accessionIds);
accessionRepository.delete(toDelete);
updateAccessionCount(institute);
}
}
......@@ -616,11 +614,11 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@Override
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = false)
public ParameterCategory addCategory(String name, String i18n) {
public ParameterCategory addCategory(String name, String i18n) {
ParameterCategory category = new ParameterCategory();
category.setName(name);
category.setNameL(i18n);
parameterCategoryRepository.save(category);
parameterCategoryRepository.save(category);
return category;
}
......@@ -628,33 +626,27 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = true)
public ParameterCategory getCategory(String name) {
ParameterCategory category =
parameterCategoryRepository.findByName(name);
ParameterCategory category = parameterCategoryRepository.findByName(name);
return category;
}
@Override
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = false)
public Parameter addParameter(
String rdfUri,
Crop crop, String category,
String title, String i18n
) {
public Parameter addParameter(String rdfUri, Crop crop, String category, String title, String i18n) {
Parameter parameter = new Parameter();
parameter.setRdfUri(StringUtils.defaultIfBlank(rdfUri, null));
parameter.setCrop(crop);
parameter.setCrop(crop);
// In an ideal world, we should search for category by URI, not name...
ParameterCategory parameterCategory =
parameterCategoryRepository.findByName(category);
ParameterCategory parameterCategory = parameterCategoryRepository.findByName(category);
parameter.setCategory(parameterCategory);
parameter.setTitle(title);
parameter.setI18n(StringUtils.defaultIfBlank(i18n, null));
parameterRepository.save(parameter);
return parameter;
......@@ -664,12 +656,17 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = true)
public Parameter getParameter(String rdfUri) {
if(rdfUri == null || rdfUri.isEmpty() )
return null ;
Parameter parameter =
parameterRepository.findByRdfUri(rdfUri) ; // assumes that crop x title is unique(?)
if (rdfUri == null || rdfUri.isEmpty())
return null;
Parameter parameter = parameterRepository.findByRdfUri(rdfUri); // assumes
// that
// crop
// x
// title
// is
// unique(?)
return parameter;
}
......@@ -677,21 +674,22 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = true)
public Parameter getParameter(Crop crop, String title) {
Parameter parameter =
parameterRepository.findByCropAndTitle(crop, title) ; // assumes that crop x title is unique(?)
Parameter parameter = parameterRepository.findByCropAndTitle(crop, title); // assumes
// that
// crop
// x
// title
// is
// unique(?)
return parameter;
}
@Override
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = false)
public Method addMethod(
String rdfUri, String description, String i18n, String unit,
String fieldName, int fieldType, Integer fieldSize,
String options, String range,
Parameter parameter
) {
public Method addMethod(String rdfUri, String description, String i18n, String unit, String fieldName, int fieldType, Integer fieldSize, String options,
String range, Parameter parameter) {
Method method = new Method();
method.setRdfUri(StringUtils.defaultIfBlank(rdfUri, null));
......@@ -700,12 +698,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
method.setUnit(StringUtils.defaultIfBlank(StringUtils.trimToNull(unit), null));
method.setFieldName(StringUtils.trimToNull(fieldName));
method.setFieldType(fieldType);
if (fieldType == 0) {
// Will throw NPE if not provided!
method.setFieldSize(fieldSize.toString());
}
method.setOptions(StringUtils.defaultIfBlank(StringUtils.trimToNull(options), null));
method.setRange(StringUtils.defaultIfBlank(StringUtils.trimToNull(range), null));
method.setParameter(parameter);
......@@ -722,26 +720,23 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@PreAuthorize("isAuthenticated()")
@Transactional(readOnly = true)
public Method getMethod(String rdfUri) {
if(rdfUri == null || rdfUri.isEmpty() )
return null ;
Method method =
methodRepository.findByRdfUri(rdfUri) ;
if (rdfUri == null || rdfUri.isEmpty())
return null;
Method method = methodRepository.findByRdfUri(rdfUri);
return method;
}
@Override
public Method getMethod(String description, Parameter parameter) {
if(description == null || description.isEmpty() )
return null ;
Method method =
methodRepository.findByMethodAndParameter(description,parameter) ;
if (description == null || description.isEmpty())
return null;
Method method = methodRepository.findByMethodAndParameter(description, parameter);
return method;
}
......
src/main/java/org/genesys2/server/servlet/controller/WiewsController.java
View file @ 9a9f0cbc
......@@ -100,6 +100,7 @@ public class WiewsController extends BaseController {
// model.addAttribute("statisticsCrop",
// genesysService.statisticsCropByInstitute(faoInstitute, new
// PageRequest(0, 30)));
model.addAttribute("statisticsGenus", genesysService.statisticsGenusByInstitute(faoInstitute, new PageRequest(0, 30)));
model.addAttribute("statisticsTaxonomy", genesysService.statisticsTaxonomyByInstitute(faoInstitute, new PageRequest(0, 30)));
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment